Time For Hope?
by PUBLISH
Summary: The mastermind was revealed, her lies exposed. But the survivors aren't ever returning to normal life again. Despair is still around the corner of the Doctor...


**AUTHOR'S NOTE: FOR THIS TO MAKE ANY LICK OF SENSE, YOU'D HAVE TO IGNORE THE SEQUEL TO THE FIRST ANIME, THIS IS AN ONE-SHOT AU WHICH WILL DEVIATE FROM THE ORIGINAL SOURCE. AS FOR DOCTOR WHO CANON, YOU MUST IGNORE THE UPCOMING SERIES TEN AS THIS IS WRITTEN BEFORE SAID SERIES AND WILL NOT BE FULLY ADDRESSED. I DO NOT OWN ANY CHARACTERS.**

* * *

 **TIME FOR HOPE?**

Seven students, the survivors of Class 78th, six of which near the entrance of the room as the seventh was strapped to her desk; the perfect parody of a student eager to for the lesson to attend. Makoto Naegi visibly flinched being in the very room that he nearly met his end in, an action that went unnoticed by everyone else but two, both with contrasting facial expressions.

One kept her eyes straight forward, eyes narrowed at the mastermind, who stared at them all with a loose grin at their despair.

Hope was described as a feeling of expectation and desire for a thing to happen. Hope is nothing more than a lie, a fantasy. She had hope once, hope that her 'other' experiments would succeed, that her people would survive the great War, a war that she would survive. Hope led her to another change, plagued with the two annoyances in her side, making a mockery of their people, of her.

But their goals remained the same, their morals stayed true throughout their lives and she knew where to strike.

Humans, his precious surrogate family one could say.

And the sound of footsteps alerted her to the primary annoyance, how his humans watched in confusion and awe as the 'detective' stopped in front of the desk, face hard, eyes narrowed but there was still a small part of the compassion she despised so much.

"Is this the final face I see before the end?" Junko Enoshima raised an eyebrow, yawning an exaggerated yawn. "BO-RING!"

"You let him take all the credit?" she asked with a scoff, her grin present as always but eyes almost lifeless. "That's so predicable of you. Even as a female."

Kyoko Kirigiri said nothing, as still as a statute.

"But did you tell them about the truth?" the blonde pressed on. "About your little…change, Doctor?"

"It's better they don't know." the Doctor spoke in Kyoko's voice, moving a loose strand of Kyoko's hair with Kyoko's gloved hand. "Your little lies back there damaged them enough."

Junko didn't change expression at the word 'lies' but only nodded as if she expected this.

"How did you know?" the third question she asked in the past two minutes without a single change in personality; there was not point now. She was exposed, her identity known.

"Oh please." it was no surprise to Junko that this incarnation of the Doctor was very much like Kyoko, her purple eyes rolling in exasperation. "You think I don't recognize a fake hologram when I see one? If this whole despair faux was true, I'd know just by looking it up."

"Tricking your-" Junko stopped herself with a dark chuckle. "I mean her father was easy. After all, we Time Lords have certain gifts."

She had to admit that when it came to the Doctor, his intellect has not changed with his appearance, still having an answer when it comes down to the 'majesty' of time. Fixed points in time were his speciality just as research was hers.

"I have to say though; I'm surprised you found the need to erase my memories AGAIN." her left hand patted her own jacket, no doubt where the Chameleon Arch fob watch laid. "But you just couldn't resist messing with me."

"It was too fun." Junko shrugged with her free hands. "I got carried away in my little experiment, I can admit that."

"Sloppy." The Doctor commented dryly. "Making both of us regenerate then using the Chameleon Arch to alter my perspective, that was genius and I can forgive that. I can forgive taking away two years of Kyoko Kirigiri. However…" there was a small pause as she glared down at the mastermind. "I can never forgive you for killing these innocents."

"Innocents who freely killed each other, Doctor." Junko said exasperatedly. "You would still defend humanity even after that?"

"Always." the Doctor nodded, eyes lingering on the machine behind Junko's restraint form. "Instant death, no regeneration. Unlike you."

"My experiment was utter despair." Junko reminded her bluntly. "Your humans will feel despair at my demise, the hope bringer especially. But the biggest prize will be that you will despair in the loss of another Time Lord."

"If you say so." the Doctor said.

Both Time Lords stared in each other in a tense silence, both set of eyes narrowed in glares. Suddenly, a whirring sound echoed across the room as Junko's desk slowly moved backwards, Junko's glare slowly forming a wide grin.

"The true despair." she whispered excitedly over the trash compactor like block's bangs, holding off the orange glow that surrounded her as she waved her hand in the air. "The end of an era. It's been fun, Doctor."

 **CRASH!**

The Doctor scrunched her noise in disgust at this.

 **CRASH!**

"It was never fun." she rebuked. "Goodbye, Master."

 **CRASH!**

She saw her eyes widened and the Doctor had her shock behind a stone face, a stone face that slowly crumbled- VERY slowly- when the traditional 'Upupupupup' like laugh left her lips. And then she spoke words that changed everything the Doctor believed up until this moment.

 **CRUSH!**

The block fell and Junko died in a splatter of blood, leaving behind five emotionally scarred humans.

Alongside one sacred Time Lord.

* * *

The Doctor was deep thought as the lift ascended, everyone else near her meant nothing now.

Of course, it was her. All an experiment. she thought to herself.

But the theatricality of it all, the bear, the executions, they all felt too much like HER. Where was she wrong, even when regenerated, there was always a lasting trait Time Lords-

She surpassed her gasp of realization.

 _Oh, stupid, stupid Doctor! You idiot! She was just more psychotic then her last life! Happens to us all._

Before she could mentally scold herself again, images flashed in her head; she was the attack eyebrows body, she- or he- was in the TARDIS of the Rani with the latter herself and a woman looking like a evil Mary Poppins.

The Master.

Words and insults were thrown at each other before the TARDIS gave a shake and her head hit the console.

The scolding continued at the shere absurdity of it all.

 _ANOTHER BANG ON THE HEAD?! AM I GOING TO NEED TO HEAR A SAFETY HELEMT EVERY TIME I-_

"Kirigiri?"

The Doctor snapped out of herself loathing at the sound of Makoto's concerned voice and she looked towards his green orbs full of that very same concern.

"Yes?" the Doctor replied in what she hoped sounded like Kyoko's normal stoic tone. "What is it? And please, call me Kyoko. I believe you earned that right."

"Well..." Aio Asahina started nervously, no doubt emotionally wrecked by the upcoming revelations. "...We were wondering what…what she said to you."

The Doctor looked towards her, complementing her answer. The truth or a lie?

"She lied." the Doctor said finally. "There is no great despair. She just said it to erase our hope."

Makoto's eyes widen as the others looked at the Doctor.

If they start saluting, I swear-

"Seriously?!" Makoto asked hopefully but the Doctor was cut off by Yasuhrio Hagakure's loud whoop.

"OH RIGHT!" he laughed heartedly. "Just as I foretold!"

"Oh please." Byakuya Togmai shot his victory claim down without even changing from his frown. "If you could foretell that, then you could have easily have realized who the mastermind was."

"Hey, give me some credit!" Yasuhrio whined.

"For what?!"

The Doctor watched the survivors of Class 78 rejoice/argue in their own little way and she smiled; a rarity for this incarnation. She saved them, just as she always did.

 _With help._ she thought to herself with a glance towards Makoto. _A genius, someone who brought hope to them all. I'm taking with me._

"We might as well spend one last night here." Byakuya said suddenly as he pulled out a fob watch from his pocket. "It's late enough as it is."

The Doctor froze seeing the fob watch, studying it from afar. Her mind was blog up and with her boots clicking, she approached Byaukya in three steps. The blonde man stared down at her in bemusement.

"Is there a reason why you're invading my personal space?" he demanded.

"That fob watch." the Doctor replied bluntly, ignoring Toko Fukawa's protests and threats of 'getting away from her man.'

"A family possession." Byaukya nodded impatiently and clicked it open.

"DON'T!" the Doctor cried out as the watch fully opened and she could only watch in horror as-

The time was nine thirty pm.

"Is there a problem?" the taller male asked sarcastically, eyebrows raised at Kyoko's uncharacteristic sheepish expression.

"No. No." she replied after a small awkward silence. "I just feel like it's a remarkable fob watch."

 _Oh, nice one(!)_

She was spared out of seeing the looks of utter confusion by the lift opening at first and she was the first to walk out.

"Goodnight, everyone." she called out but she thought differently.

 _So he's not a Time Lord..could it be possible that -_

 _..._

 _Pull yourself together, she had to be lying, she had to be._

Yes, that had to be it; the Master would always lie; always! He/she is dead now. And all the Doctor could focus on was getting these humans home safely.

Though the Doctor didn't hear the sneeze, she could hear Genocide Jill calling her a 'mad bitch'.

 _I prefer a mad woman._ she corrected in her mind. _Mad woman in a box. Speaking of which, where are you, sexy?_

* * *

Nobody felt comfortable sleeping in Hope's Peak Academy another night after the weeks- or rather two years- of hell they suffered. Some had nightmares while others didn't feel tired and wanted to left the building as soon as possible. But the Doctor wasn't fast asleep at all; instead she was in the gym, looking around for her beloved ship.

It was hard to believe everything that happened, even for her. Becoming human, losing two years of her false life. Becoming a girl! She just wanted to get out of this. How would she do this? By moving her hands around as if trying to touch something.

"Where did you park it?' she muttered quietly in the dark. "Come on, old girl."

She didn't feel anything yet. If anyone was watching, they would calm the girl lost her mind. That wasn't true at all; she was already mad. The Time Lord felt a tinge of eagerness when her hand touched something invisible.

 _There you are._

Raising the same thing, she snapped her fingers and a blue police box shoe into existence, the double doors opening at once. Slowly, the Doctor stepped in, taking in the features of her long-lasting companion; it no longer looked like a normal control centre with little bookshelves everywhere. Instead, the room resembled a Victorian style library with statutes, clocks of all sorts and a cozy little arm chair just near the wooden console in the middle of the room.

"You redecorated." the Doctor voiced the nostalgia she felt. "I love it."

Her lips twitched a bit when she gently stroked the console, as slow as her steps into the box.

Her home.

Her friend.

Her TARDIS.

"Least she didn't touch you." she said quietly as though to a lover. "I been so busy, being human." her face was crunched up a bit. "But we can go now. Anywhere we- "

"Kyoko?"

The Doctor froze for a moment. What was someone else doing out of their room now of all times?! She slowly turned to see Makoto standing outside the door, mouth agape at the room.

"W-what is this?" he asked with unsteady breathing. "Is this- "

"No." the Doctor answered the question before even asked. "This isn't one of Junko's games, it's my ship and yes, it's bigger on the inside."

Makoto hesitated when he saw 'Kyoko' jerk her head, inviting him. The brown-haired boy was clearly scared of any trap but his trust in the girl was stronger and he hesitantly stepped in, eyes darting towards every part of the room in a mixture of dread and awe.

"It's called the TARDIS." the Doctor announced, leaning on the console. "It's a time machine. It can go anywhere through time and space." she paused for dramatic effect. "And its mine."

"K…Kyoko-"

Now came the hardest part: admitting the truth.

"Kyoko Krigiri never existed." the Doctor said bluntly and started to regret it seeing Makoto step back in shock. In a unKyoko action, the Time Lord stepped forward, hands in front her. "But I thought I was because of Junko's memory wipe, I swear to you."

"…Then who are you?" Makoto questioned in suspicion.

 _Oh, I love it when they ask that._

"I'm the Doctor." Kyoko Kirigiri declared and for more dramatic effect, the TARDIS lit up the candles in the room. "I'm a Time Lord from Galifrey. And I am your friend."

But Makoto just stared at her with those wide green eyes and mouth agape. The Doctor sighed at this.

"Makoto Naegi." she started to walk towards him. "I promise you I'm still the girl you met. I can get everyone out of here right now but I need you to trust me."

She slowly raised one her pinkies and Makoto slowly locked his own pinkie with hers; an old promise between the two.

"I trust you, Kyo- I mean, Doctor." the young boy corrected himself.

"If you're comfortable with Kyoko, you can call me that." the Doctor said in an assuring tone. "I had a friend who called me Professor."

"Are you sure? I mean, I don't want to seem rude now that I know the truth." Makoto said sheepishly as he rubbed the back of his head.

"I am sure. Besides you are the only one here who know about me currently." The Doctor pointed out. "The others."

Her eyes widen in remembrance.

"Oh! I'm an idiot!" she suddenly yelled making Makoto yelp. "This old ship has bedrooms; we don't have to sleep in Death School 101 for another night."

Oblivious to her friend's distress, the Doctor held a small device in her hand. A small whirring sound and suddenly her voice was heard through every speaker in the school.

"May everyone please come to the gym?" the Doctor spoke into the sonic screwdriver as stoic as the detective they believed her to be.

"There is something I need to show you."

She glanced back towards Makoto who offered his trademark bright smile and she smiled back slightly.

"We're getting out of here." the Doctor said .

"...What bout you?" Makoto asked. "What about after we leave?"

"I will travel through time and space." the Time Lord answered with a small smile. "You can join me if you wish."

The Doctor thought the grin spreading across the young boy's face was just adorable-

 _Let's not go that far, Doctor. You're married. Heel, girl._

Regardless, she clapped his shoulder with more affection than she should walked out. "Help yourself to the jelly babies."

Once she was out, the doors closed behind her. Makoto glanced towards the armchair and table .

"In a ashtray?" the boy asked out loud as he took a jelly baby out of said ashtray once he took a seat. Instantly his face lit up.

Sour but satisfying.

"All of time and space..." Makoto repeated with his mouth few. "Where are we even gonna start?"

* * *

The survivors had arrived drowsy and tired in the gym to 'Kyoko' standing on the podium, who seemed to be have some sort of renewed energy.

"Hey, man, this better be worth waking us up as three in the morning." Yasuhrio half-yawned.

"Yeah, was in the middle of one of THOSE dreams bout my MAN!" Genocide Jill snapped, clearly full of energy.

"Trust me, I wouldn't have woken you up if it wasn't important." 'Kyoko' answered.

"Then what is it?" Byaukya asked impatiently.

'Kyoko took a deep breath before she answered.

"You all have expressed distrust and suspicions of me. I do not blame you." the purple haired girl said. "Because I am not Kyoko Krigiri."

"Eh?" Ain asked in a mix of shock and confusion.

"If you're not Kyoko Kirigiri than who are you?" Byakuya asked coldly.

"Your planet has been invaded so many times and I always been there." 'Kyoko' said, moving her arms up. "I am the saviour of human kind. I am..the Doctor."

* * *

"Kyoko actually lives here?" Makoto mused, glancing at blue light the console illuminated. "Man, that girl is really full of surprises…but how much of her do I actually know?"

He recalled how she said she had lost her memories outside of the name 'Kyoko Kirigiri'. The fact she was just now suggesting using the machine to get out of the school with everyone still alive helped show that detail was true. But that also leave questions for the young boy: why did The Doctor come to the school? Did the mastermind know the truth behind 'Kyoko' or was it just pure luck the Time Lord got caught in the deadly game? Speaking of the mastermind, why did she talk to Junko? Gloating was out of character for Kyoko; at least he thought it was.

* * *

"Doctor Who?" Yashiro scratched his head but the Doctor was cut off by her least favorite blonde human.

"So you confess to more secrets?!" the Togmai heir demanded. "What do we actually know about you then if you are not the girl you masqueraded as?"

"I am the Doctor." she repeated, eyes lingering on their confused and untrusting gazes, harder to convince than Makoto. "My memories as Kyoko are all fake. But I am still the same girl. In a way."

* * *

Makoto sighed to himself. Just when he thought he was beginning to know her, she ends up being a Time Lord, whatever that was. Kyoko just acted randomly now; more emotional and dramatic, having a interest in fob watches.

"Maybe she'd be interested in mine." Makoto pulled his own out of his pocket; just like Byakuya's in shape but had strange circular like symbols carved on. "Doesn't even work but-"

He stopped suddenly as if just realizing something important.

What, exactly?

He never had a fob watch.

* * *

The Doctor looked at Jill, hearing her scoff.

"Is there a problem?" the Time Lord asked, knowing there would be.

"You start calling yourself some other name to sound badass and interrupt my dream of MY MAN for THIS!" she twirled her scissors in anger, face right red.

"I agree with her for once. This is ridiculous." Byaukya crossed his arms in irritation.

"If proof is what you need to believe me than I do have it." the Doctor explained and leant back, her back hitting the air. A second later, she held back a grin seeing Aio gasp at the sight of the TARDIS. "

"Hey hey!" Yashiro went bright red in the face. "I don't go into small boxes with a girl-"

"It's our ticket out of here." the Doctor cut off with a cold look at the implication of her ship's true purpose. For the second time that night, she snapped her fingers.

* * *

Makoto stood from his chair, staring down at the fob watch in his palm, everything else a blur. So many questions ran through his head: what is this doing here? Whose is it? Why is he only now seeing something wrong?

It was strange how he had no answer to any of those questions, his original assumptions were that it was a gift from his parents or that he received it the two years he could not remember but non of those answers felt right.

 _ **Open up.**_

Makoto turned abruptly, swinging his head towards every direction.

"Hello?" he called. "Kyoko?"

A small of him dreaded that perhaps the bear was back and would attack so he stood anxiously for minutes on edge. Silence answered and he quickly looked back towards the fob watch, reaching a ludicrous conclusion.

The watch was talking to him.

But..surely that was ridiculous, right?

Even more ridiculous than being talked in a school with a talking bear robot, more ridiculous than the over the top executions, more ridiculous the mastermind surriving all previous executions before the last one finally killed her?

More ridiculous than Kyoko being a 'Time Lord'? He heard the doors of the TARDIS open, he heard the gasps of awe over their footsteps, he heard Byaukya's "What is all this?!" laced with uncertainty but still didn't turn his attention from the watch, the reactions nothing but the sound of buzzing in his ears.

"Naegi?" Aio sounded concerned at the lack of a reply. Even the sound of Kyoko- the Doctor- walking to his side didn't make him look up.

"Makoto-"

Makoto Naegi suddenly felt a stab of anger at the sound of his given name by the Doctor and his hand shook, clutching the fob watch tightly.

And it opened.

* * *

"HOLY SHIT!" Yasuhiro shouted in pure shock.

"It's my ship." the Doctor said over the yells.

"What is all this?!" Byuakya demanded to know, taking a step forward into the console room. "Some sort of...of…" he faltered at just how...how sophisticated it all looked. "What is all this?!" Byuakya demanded to know, taking a step forward into the console room. "Some sort of..of…" he faltered at how sophisticated it all looked. "Are there any other rooms like this?"

The Doctor nodded only once, seeing the heir hid his eagerness with a stern look of sastisfaction. One sneeze and Toko looked around nervously, unlike her other friends.

"W-here.."

"Makoto will fill you in." the Doctor brushed her aside. "Sit down, we're getting out of here."

But when the Time Lord turned to the console, she saw Makoto with his back turned to them, as still as statute. Frowning deeply, the Doctor saw the boy looking down at something through his reflection on the time rotor.

Makoto?" Aio asked in concern.

No reply.

This isn't like him.

The Doctor slowly stood to the side of the console to see what Makoto was staring at.

And her eyes widen in utter horror.

"Naegi." she said so quietly she didn't hear herself.

 _No, no, no, no...not him. Oh, Rasslion, NOT HIM!_

"Makoto, don't-"

But the fob watch suddenly snapped open and Makoto's face was bathed in a orange light, his eyes remaining transfixed on the inside of the watch. The others covered their eyes at the exposure of the light but Aio screamed when the Doctor threw a punch at the Ultimate Lucky Student.

The Doctor grit her teeth at the all too familiar light, her mind spiralling with old memories of a very similar event; she was in what she called the 'Edward Cullen' incarnation, vain and so full of himself he believed himself to be as human as the ones he hid among. He stood in the middle of a futuristic laboratory, staring down at an elderly man right outside the TARDIS, his once gentle and kind eyes narrowed with malice and the intent to conquer.

When Makoto finally looked towards the Doctor, he too shared the exact same look. The Doctor threw a punch to the face that floored him out cold, the watch landing in her palm.

"Kyoko!" Aio screamed in surprise. "What is the matter with you?!"

"Dude, have you gone crazy!" Yasuhiro yelped.

"What is the meaning of this?!" Byuakya demanded, eyes narrowed. "Why did you attack him? What was all that?!"

"Chameleon Arch." the body that claimed to be Kyoko Kirigiri said coldly, her eyes downcast at the fob watch pretending she could melt it just by staring at it. "It alters the biology of anyone. With this, you become any other species, the real you locked inside this fob watch equipped with a perception filter to avoid detection." her hand shook. "That's why I checked yours. I had to be sure you were not the monster inside this."

"So you and Makoto are not human?" Byuakya huffed. "Forgive me for being in disbelief, but I find it hard to believe both of you are Lords of Time."

"Junko was the third." the Doctor's revelation made the classmates' eyes widen, reflecting on the conversation they could not hear before the mastermind's execution. The Doctor, on the other hand, replayed the last words of Junko over and over in her head.

 _My name's the Rani._

Rani.

Rani.

"The Rani was Junko the entire time." she spoke up. "I am the Doctor."

"And Makoto?" Toko whimpered, clutching her hair. "Who is he-"

"Makoto Naegi is Makoto Naegi." the Doctor cut off sharply, glancing towards the out cold boy. "That punch should have given him a nasty headache, enough time for me to erase his memory of the fob watch and hopefully of the monster from the watch."

"So you're going to subject him to the very thing that mad woman did to us?!" Byuakya was seething at the very thought. "Towards your so-called friend."

The Doctor frowned darkly as she heaved Makoto's body over her shoulder gently.

"Would you rather be subjected to be more mind games by him?" she questioned, her purple eyes violating the blonde's very soul. "Would you rather be the plaything of the _Master_?!"

* * *

 **END CHAPTER**

 **Yep. This is one of those stories. The first actual DaganRonpa and Doctor Who crossover. As I stated before, this is a AU set in my own universe of each franchise, the second anime of the former never happened and the upcoming series 10 and those after it have never happened. Sorry if it got confusing at the end , I was trying to show different reactions and stuff happening roughly at the same time.**

 **Now for my reasons for each Time Lord used:**

 **Kyoko as the Doctor: I admit, I always had this thought as soon as I saw the show; the attitude, the clothes, the intellect all screamed Doctor to me. Plus, unlike the show, I'm not gonna be cracking jokes about the Doctor being a girl a LOT.**

 **Junko as the Rani: Her experiments and the whole school being one crazy experiment; how could I even resist. Plus, a crazy Rani, we never had that.**

 **Makoto as the Master: This was largely expired by the new series deception of the Master and Doctor relationship. I'd imagine that the Doctor now would want to keep Makoto from becoming the Master as a way to make up for the years of conflict. And yes, she will make very questionable decisions to ensure this. Oh, but when Makoto does become the Master, expect a bit of John Simm and Alex McQueen in this incarnation.**

 **Special thanks to a friend from Deviantart for the help.**

 **Hope you all enjoyed. Please R and R, hell if you'd like to do stories based off this idea, go ahead. Heck, I'd even co-write with ya.**


End file.
